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1499: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1499: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed
Created: 03/20/2018
Points: 0
Expired: 03/27/2018 - 23:00
Difficulty: Intermediate
Description: This symmetric design puzzle has C2 symmetry, with two symmetric chains. The H-bond Network Filter encourages players to bury satisfied H-bond networks at the interface between the two chains. There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

Note: This puzzle was closed early due to a problematic filter, and reposted as Puzzle 1499b.
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Comments

bkoep's picture
User offline. Last seen 11 hours 3 min ago. Offline
Joined: 11/15/2012
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Filters

Core Existence: Monomer: Ensures that at least 25% residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 30% residues are buried in the core of the entire complex (including the interface between monomer units).

HBond Network: Rewards networks comprising at least three hydrogen bonds. Up to four hydrogen bonds may span the interface between chains. Networks must at least 50% satisfied (i.e. 50% of all polar atoms in a network must make a hydrogen bond).

NinjaGreg's picture
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Joined: 05/21/2010
Groups: Go Science
Select all then mutate crashes consistently on mac - workaround

To get around this crash, just before invoking mutate ("Y"), move the protein completely off-screen (out of view in the window), then invoke mutate. It runs until you stop it then.

You move the protein by right-clicking on the background, holding the click down, and dragging the protein off the edge as far as possible, then releasing the click. You may have to repeat this motion a couple of times to get it completely off, depending on where you initially click on the background.

The crash is in the drawing code (NormalizeVector routine, I believe), so if there's nothing to draw you don't hit the error condition.

bkoep's picture
User offline. Last seen 11 hours 3 min ago. Offline
Joined: 11/15/2012
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Unable to reproduce

Thanks for the feedback! I'm having hard time reproducing this crash. Does it happen with all solutions (even the starting structure)?

I'm also curious to see the Foldit log file. If you don't mind making a Feedback and uploading your log file, that would be really helpful for tracking down this bug.

Joined: 09/24/2012
Groups: Go Science
Strange behaviour of the monomer core filter

When I work on a monomer (the symmetric chain far away), the complex core filter goes ok before the monomer filter. This is counterintuitive. Is it normal?

bkoep's picture
User offline. Last seen 11 hours 3 min ago. Offline
Joined: 11/15/2012
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Possible, yes

The complex core filter in this puzzle is using a slightly different threshold to decide which residues are "core" and which are not. So it's possible that some residues are considered "core" by the complex filter, but not with the monomer filter—even when the symmetric chains are far apart.

This suggests that the filter settings are a little off, and need to be retuned. This is helpful feedback, thanks!

Joined: 09/21/2011
Groups: Void Crushers
Or maybe just the filter names are reversed

See the title

bkoep's picture
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Joined: 11/15/2012
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Filters named correctly

The filters are named correctly; they are just configured poorly.

The Monomer Filter requires only 25% core residues, and the Complex Filter requires 30% residues. The idea here is that you can make up the difference of 5% with residues that are at the interface (i.e. these residues would be exposed on the monomer, but buried in the complex).

The problem, pointed out by Bruno, is that the Complex Filter has a different threshold for what makes a "core" residue. In effect, even when the symmetric chains are far apart, some "almost core" residues do not meet the threshold for the Monomer Filter, but they will meet the threshold for the Complex Filter. If you click the "Show" checkbox for each of these filters, you will probably see that some residues are green for the Monomer Filter and orange for the Complex Filter.

This is a configuration we had used in previous symmetry puzzles, but it seems some things have changed to make the effects more pronounced. We won't close this puzzle (players should still be able to satisfy both filters!), but in future puzzles we'll make sure both filters are using the same thresholds.

Joined: 09/21/2011
Groups: Void Crushers
Still I think that the monomer penalty is incorrect

Given 25% of 70 times 100 equals 1700 rounded down not 3700 like it is now. Maybe a typo?

bkoep's picture
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Joined: 11/15/2012
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You're right!

Thanks for clarifying—I had assumed the threshold issue was the source of all the problems. This looks like it might be a bug. The filter is set at 25% core, but it's behaving like it expects 50% core.

This should be easy enough to get around. We'll close and repost the puzzle.

jeff101's picture
User offline. Last seen 16 hours 16 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Quirky tricks & some ideas for symmetry puzzles:

In this puzzle, I often had trouble finding a monomer. Using View/Show Symmetric Chains made my chances higher. Neither Home nor Q would reliably bring a monomer into view. I think it would help if Home or Q would bring the original monomer into view.

Once I got a monomer on the screen, rotating & translating it around was tricky. I found mouse Q and mouse shift Q to help with this. They focus the rotation & translation on where you put the mouse when you press Q or shift Q. One of them (mouse shift Q?) often chopped off parts of the protein. Usually this bothered me, but it can help if you want to look at features inside the protein.

I found I could tab on residues in each monomer. I could even add Notes to the copied monomer different from Notes I put on the original monomer. Using Note Mode put these Notes on the screen, and if the monomers were off-screen, these Notes showed in which direction each monomer was.

I think it would help if there were arrows pointing in the direction of each monomer when the monomers reside off the screen. Another idea is to have a line segment (like a disabled band) always connecting the monomers to each other. Then, if you can find one monomer, you can always follow the line to the other one. If there were 3 monomers, there could be 3 such lines between monomers 1-2 2-3 and 3-1, making a big triangle. For 4 monomers, use 4 lines to connect monomers 1-2 2-3 3-4 and 4-1.

Joined: 09/21/2011
Groups: Void Crushers
Using cut and move broke the sym

The move did nothing on the original but moved the shadow. See: http://fold.it/portal/files/chatimg/irc_308854_1521657120.png
Strangely when I saved it and reloaded the sym was back and move worked as expected.

bkoep's picture
User offline. Last seen 11 hours 3 min ago. Offline
Joined: 11/15/2012
Groups: None
Definite bug

Is this reproducible? Can you share that solution with scientists?

Joined: 09/21/2011
Groups: Void Crushers
I can not reproduce it

As I wrote, after saving and reloading the shadow was the same as the original. The original did not change there, the shadow became equal to the original. So a very strange glitch. And the scientists will not have info from the save I think.

Joined: 06/24/2008
Groups: Void Crushers
Bug

I just sent to Scientist what i think maybe a bug. I was making sheets -7- and the last three can not be moved by the move tool.

Joined: 09/21/2011
Groups: Void Crushers
When you save and reload would that help?

Looks like the same kind of problem I had.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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